+
Sequence Feature Settings for the Jalview Application
The top section of the dialog box lists all the sequence feature groups, along with a tickbox for each that controls whether its features are displayed. The table in the middle lists all the features in the -currently selected groups, along with their display colour and whether +currently selected groups, along with their display style and whether they are currently being displayed (only the ticked features and groups -are displayed). You can change the colour used -for a feature in the associated alignment by clicking on its colour box.
+are displayed). You can change the colour or +shading style used for a feature in the associated alignment by clicking +on its colour box. +
+ Selecting
+ alignment columns by feature
Double-clicking
+ a feature type in the Feature
+ Settings dialog allows you to select columns in the
+ alignment that contain (or do not contain) features of that type. If a
+ region of the alignment is currently selected, then only features in
+ the current selection will be searched. The following keys affect the
+ way in which selections are made:
-
+
- Hold down Alt to select columns not + containing features of a particular type. + +
- Hold down Shift to add columns to the + current selection. + +
- Press Command/Windows key to toggle column + selection state (XOR) + +
+ Select columns by feature was added in Jalview 2.8.1 + +
Feature settings pop-up menu
+Right-click on a feature to open a pop-up menu that
+allows you to sort the alignment or current selection using that feature
+type (see below), or toggle the type of colouring used for the feature.
+Features may be highlighted with either a single colour or a feature colourscheme based on either the
+scores associated with that feature or from the feature's description
+(e.g. to distinguish different names associated with a DOMAIN feature).
Ordering alignment by features
-Right click on a feature type to order the alignment by either the
-feature's score, or the number of features of that type. The 'Order by
-Score' and 'Order by Density' buttons will order the alignnment based on
-the average score or total number of currently active features and
-groups on each sequence. (Experimental - added in jalview 2.4.1)
+Feature sorting and graduated feature colouring were introduced +in Jalview 2.5 +
Transparency and Feature Ordering
It is important to realise that sequence features are often not distinct and often overlap (for example, a metal binding site feature may be attached to one position along a stretch of sequence marked with a secondary structure feature).
The ordering of the sequence features in the dialog box list is
-the order used by jalview for rendering sequence features. A feature at
+the order used by Jalview for rendering sequence features. A feature at
the bottom of the list is rendered below a feature higher up in
the list.
You can change the order of a feature by
@@ -44,10 +99,6 @@ visibility of features rendered below other features. Reducing the
transparency will mean that features at the top of the list can obscure
features lower down, and increasing it allows the user to 'see through'
the upper layers of a set of features.
Right-click on a feature to open a pop-up menu -that allows you to sort the alignment or current selection using that -feature type, or create a graduated feature colourscheme based on the -scores associated with that feature.
You can save all features, with their current colours and visibility in a Jalview format file.